I know about the well known issue with water intrusion through the 3rd brake light. Mine had this issue when I bought it so I fixed it.
Now I'm noticing water in the back drivers side corner. Through some searching I have seen people have issues with the rear window seals failing. I'm thinking this may be my issue but before I pull the rear window I'm curious if because the truck is missing the black cab corner trim if water could be entering from there?
Turns out the rear window was replaced at one point and was either installed wrong or gasket material had failed. After removing the window, cleaning the area and reinstalling it using 3M butyl the water intrusion has stopped.